[R-pkg-devel] how to use pkgdown::build_site() with a project using S7 with a specialized plot()?

Wed Jan 3 18:06:11 CET 2024

This bug is fixed in the dev version (I don’t remember off the top of my
head in which of pkgdown and roxygen2 you need but it might be both). I’m
planning CRAN updates for both in the near future.

Hadley

On Thursday, January 4, 2024, Daniel Kelley <kelley using dal.ca> wrote:

> # Question
>
> Is there an online example online of specializing `plot()` for S7 objects,
> such that `pkgdown::build_site()` will produce webpages?  I ask because I
> find lots of users (of other packages) tend to consult websites made with
> pkgdown, rather than using the online help within R.  I think the problem I
> am having (discussed in the following sections) has to do with my
> specialization of plot().  I say that because when I was using S3 objects
> in an earlier version of my package, `pkgdown::build_site()` worked as
> intended.
>
> # Background
>
> In my 'mooring' package (https://github.com/dankelley/mooring/tree/S7), I
> am writing code like (https://github.com/dankelley/mooring/blob/
> f70b53ca12e88968f65710c205b50a64f750a99d/R/plot.R#L69)
>
> ```R
> #' @aliases plot.mooring
> #' ETC
> `plot.mooring::mooring` <- plot(ETC) ETC
> ```
>
> to handle objects made with (https://github.com/dankelley/mooring/blob/
> f70b53ca12e88968f65710c205b50a64f750a99d/R/oo.R#L2)
>
> ```R
> mooringS7 <- S7::new_class("mooring",
>     package = "mooring",
> ETC
> ```
>
> Built up in Rstudio, with Roxygen2 being used to create documentation,
> things seem to work, e.g.
>
> ```R
> m <- mooring(anchor(), wire(length = 80), float(), waterDepth = 100)
> plot(m)
> ```
>
> produces a plot as intended, and
>
> ```R
> ?plot.mooring
> ```
>
> produces documentation as intended.
>
> *However* I encounter a problem comes when I try building a website with
>
> ```R
> pkgdown::build_site()
> ```
>
> This yields results as in the next section.  (I apologize for the length.
> I'm including the whole thing because I thought that would be less
> bothersome than writing another email to the list.)
>
> I am not sure how to find the problem, and so I hope that someone on this
> list can point out an example of how to set up `plot()` to work with S7
> objects, in such a way that documentation can be created with Roxygen2 and
> websites can be made with `pkgdown::build_site()`.
>
> # What pkgdown::build_site() gives
>
> ```
> > library(pkgdown)
> > build_site()
> Warning: Failed to parse usage:
>
> S3method(`plot`, ``mooring::mooring``)(
>   x,
>   which = "shape",
>   showInterfaces = TRUE,
>   showDepths = FALSE,
>   showLabels = TRUE,
>   showDetails = FALSE,
>   fancy = FALSE,
>   title = "",
>   mar = c(1.5, 3.5, 3.5, 1),
>   mgp = c(2, 0.7, 0),
>   xlim = NULL,
>   xaxs = "r",
>   yaxs = "r",
>   type = "l",
>   debug = 0,
>   ...
> )
>
> -- Installing package into temporary library ----------------
> == Building pkgdown site ==============================
> =========================
> Reading from: '/Users/kelley/git/mooring'
> Writing to:   '/Users/kelley/git/mooring/docs'
> -- Initialising site ------------------------------
> -----------------------------
> -- Building home ------------------------------
> ---------------------------------
> Writing '404.html'
> -- Building function reference ------------------------------
> -------------------
> Error:
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.
> ℹ See `$stdout` for standard output.
> Type .Last.error to see the more details.
> > .Last.error
> <callr_error/rlib_error_3_0/rlib_error/error>
> Error:
> ! in callr subprocess.
> Caused by error in `map2(.x, vec_index(.x), .f, ...)`:
> ! In index: 1.
> ℹ See `$stdout` for standard output.
> ---
> Backtrace:
> 1. pkgdown::build_site()
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, run…
> 3. callr::r(function(..., cli_colors, pkgdown_internet) { …
> 4. callr:::get_result(output = out, options)
> 5. callr:::throw(callr_remote_error(remerr, output), parent = fix_…
> ---
> Subprocess backtrace:
>  1. pkgdown::build_site(...)
>  2. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do…
>  3. pkgdown::build_reference(pkg, lazy = lazy, examples = examples, …
>  4. pkgdown::build_reference_index(pkg)
>  5. pkgdown::render_page(pkg, "reference-index", data = data_referen…
>  6. pkgdown:::render_page_html(pkg, name = name, data = data, depth =…
>  7. utils::modifyList(data_template(pkg, depth = depth), da…
>  8. base::stopifnot(is.list(x), is.list(val))
>  9. pkgdown:::data_reference_index(pkg)
> 10. meta %>% purrr::imap(data_reference_index_rows, pkg = p…
> 11. base::unlist(., recursive = FALSE)
> 12. purrr::compact(.)
> 13. purrr::discard(.x, function(x) is_empty(.f(x)))
> 14. purrr:::where_if(.x, .p, ...)
> 15. purrr:::map_(.x, .p, ..., .type = "logical", .purrr_error_call …
> 16. purrr:::vctrs_vec_compat(.x, .purrr_user_env)
> 17. purrr::imap(., data_reference_index_rows, pkg = pkg)
> 18. purrr::map2(.x, vec_index(.x), .f, ...)
> 19. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
> 20. purrr:::with_indexed_errors(i = i, names = names, error_call = …
> 21. base::withCallingHandlers(expr, error = function(cnd) { …
> 22. purrr:::call_with_cleanup(map2_impl, environment(), .type, .pro…
> 23. local .f(.x[[i]], .y[[i]], ...)
> 24. pkgdown:::section_topics(section$contents, pkg$topics, pkg$src_pa…
> 25. base::rbind(topics, ext_topics(ext_strings))
> 26. base::rbind(deparse.level, ...)
> 27. pkgdown:::ext_topics(ext_strings)
> 28. purrr::map2(pkg, fun, get_rd_from_help)
> 29. purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
> 30. purrr:::with_indexed_errors(i = i, names = names, error_call = …
> 31. base::withCallingHandlers(expr, error = function(cnd) { …
> 32. purrr:::call_with_cleanup(map2_impl, environment(), .type, .pro…
> 33. local .f(.x[[i]], .y[[i]], ...)
> 34. rlang::check_installed(package, "as it's used in the reference…
> 35. base::stop(cnd)
> 36. (function (cnd) …
> 37. cli::cli_abort(message, location = i, name = name, pare…
> 38. | rlang::abort(message, ..., call = call, use_cli_format …
> 39. | rlang:::signal_abort(cnd, .file)
> 40. | base::signalCondition(cnd)
> 41. (function (cnd) …
> 42. cli::cli_abort(message, location = i, name = name, pare…
> 43. | rlang::abort(message, ..., call = call, use_cli_format …
> 44. | rlang:::signal_abort(cnd, .file)
> 45. | base::signalCondition(cnd)
> 46. global (function (e) …
> ```
>
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>

-- 
http://hadley.nz

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